SGCD
protein-codingsarcoglycan delta
Gene summary
The protein encoded by this gene is one of the four known components of the sarcoglycan complex, which is a subcomplex of the dystrophin-glycoprotein complex (DGC). DGC forms a link between the F-actin cytoskeleton and the extracellular matrix. This protein is expressed most abundantly in skeletal and cardiac muscle. Mutations in this gene have been associated with autosomal recessive limb-girdle muscular dystrophy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding distinct isoforms have been observed for this gene. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~897.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0011028
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0015470
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0015152
Submitter: ClinGen
SGCD was first reported in relation to autosomal recessive limb-girdle muscular dystrophy in 1996 (Nigro et al., PMID: 8841194). At least eight variants (e.g. missense, nonsense, frameshift, etc) have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data, segregation data, and experimental data. Variants in this gene have been reported in at least eleven probands in seven publications (PMIDs: 8841194, 19259135, 20623375, 10838250, 10735275, 9832045, 30733730). Variants in this gene segregated with the disease in eight additional family members and many other heterozygous carriers. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism for disease is protein loss of function, with the loss or disruption of δ-sarcoglycan causing disruption and mislocalization of the sarcoglycan complex which causes destabilization of the sarcolemma and the resulting muscular phenotypes (PMID: 26709803). Of note, this gene has also been implicated in dilated cardiomyopathy which has been assessed separately.This gene-disease association is supported by two KO mouse models, expression studies, a partial mouse rescue, and intercellular protein interactions. The KO mouse models provide strong evidence by recapitulating the observed phenotypes in humans and a partial rescue in one was performed via restoring some of the wildtype SGCD functionality via embryonic stem cells. Expression evidence clearly links the protein to skeletal and cardiac muscle where phenotypes are observed. Finally, the protein physically interacts with all the other sarcoglycans which are all associated with AR LGMD when their function is affected. In summary, SGCD is definitively associated with autosomal recessive limb-girdle muscular dystrophy. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Limb-Girdle Muscular Dystrophy GCEP on April 10, 2020 (SOP Version 7). This gene curation was re-approved and published on 11/14/24 by the Muscular Dystrophies and Myopathies GCEP to reflect the change in the panel's name from LGMD GCEP to MDM GCEP. As part of this process, the genetic evidence was re-scored in accordance with SOP version 11.
Inheritance Pattern: AR
Disease ID:MONDO:0015152
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0011028
Submitter: Myriad Women's Health
Inheritance Pattern: AD
Disease ID:MONDO:0016333
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0011028
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0011702
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011702
Submitter: ClinGen
SGCD was originally evaluated for DCM by the ClinGen DCM GCEP on 22 November 2019. Evidence of the association of this gene with DCM was re-evaluated using SOP v10 on 30th March 2025. At the time of recuration there are minimal changes in score and new evidence; Therefore, the clinical validity classification did not change and remains Limited. A summary of the information contributing to the classification of this gene at the time of re-evaluation is summarized herein. SGCD was first reported in relation to autosomal dominant dilated cardiomyopathy in 2000 (Tsubata et al, PMID 10974018). Human genetic evidence supporting this gene-disease relationship includes case-level data. At least 30 variants (20 missense, one splice, one nonsense, two frameshift, three deletion and three intronic polymorphisms) have been reported in humans. Though most of these variants are found too commonly to explain disease. Variants in this gene have been reported in at least 33 probands in 11 publications (Tsubata et al, 2000, PMID: 10974018; Karkkainen et al, 2003, PMID: 14564412; Sylvius et al, 2003, PMID: 12794684; Baydar et al, 2016, PMID: 27488758; Bauer et al, 2009, PMID: 19259135; Chen et al, 2015, PMID: 26720722; Hata et al, 2019, PMID: 31024045, Alimohamed et al, 2023, PMID: 36270459, Shen C. et al. 2022, PMID: 35284542, Escobar-Lopez L. et al. 2021, PMID 34674813, Pugh TJ, et al. 2014, PMID: 24503780). A variant (S151A) in this gene segregated with disease in 2 additional family members. However, the S151A variant occurs too frequently to explain disease and alternative genetic causes of disease in the family were not ruled out. This gene-disease relationship has been studied in at least one case-control study (Mazzarotto et al, 2020, PMID: 31983221) at the aggregate variant level. There was no enrichment of SGCD found in the DCM cohort compared to controls (p=0.74). In addition, this gene-disease association is supported by multiple animal models (pig, hamster, mouse and drosophila), expression studies, and rescue studies in two mouse models. SGCD has also been implicated in autosomal recessive Limb Girdle Muscular Dystrophy (LGMD) which has been assessed separately (definitive, November 14, 2024). Although this gene-disease assertion is supported by experimental evidence, there is not convincing evidence directly implicating this gene in humans. In summary, there is limited evidence to support this gene-disease relationship. More evidence is needed to support the relationship of SGCD and AD DCM. This classification was approved by the ClinGen Dilated Cardiomyopathy Working Group on 30th March 2025 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0011028
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Musculoskeletal
Intervention: Cardiovascular
Rationale: The condition can include severe cardiac manifestations, and knowledge may allow surveillance (eg, with EKG, echocardiogram, and Holter monitoring) and early medical management, which may ameliorate morbidity and mortality; Heart transplantation may be indicated in individuals with severe dilated cardiomyopathy
Comments: Digenic inheritance (with SGCB) has been suggested, but the evidence is unclear
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SGCD variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000337.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 130 | 3 | 136 | ||
| missense | 1 | 2 | 188 | 7 | 198 | |
| nonsense | 15 | 4 | 4 | 23 | ||
| start loss | 1 | 1 | ||||
| frameshift | 13 | 11 | 1 | 25 | ||
| splice donor/acceptor (+/-2bp) | 1 | 11 | 10 | 22 | ||
| Total | 30 | 28 | 207 | 137 | 3 | 405 |
Highest pathogenic variant AF is 0.000022561024
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000328.2 | 8 | MANE Select | |
| Ensembl | ENSP00000338343.4 | 8 | MANE Select | |
| RefSeq | NP_001121681.1 | 7 | Standard | |
| RefSeq | NP_758447.1 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| sgcd | Danio rerio | Structure: ventricular myocardium Quality: decreased contractility abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Dilated cardiomyopathy (DCM) - Homo sapiens (human)
- Viral myocarditis - Homo sapiens (human)
- Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human)
- Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human)
- Arrhythmogenic Right Ventricular Cardiomyopathy
Biological Process
- muscle organ development
- cell death
- calcium-mediated signaling
- cellular protein-containing complex localization
- cardiac muscle tissue development
Cellular Component
- cytoskeleton
- plasma membrane
- dystrophin-associated glycoprotein complex
- sarcoglycan complex
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000337851
- Coding exons
- 8
- Length
- 897446
- Individuals with no LoFs
- 124625
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 124637
- p
- 0.0000481
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.195 | 144 | 151 | 0.955 | 0.00000775 | 1842 |
| Missense (PolyPhen) | 44 | 50.692 | 0.86799 | 641 | ||
| Synonymous | -0.181 | 61 | 59.2 | 1.03 | 0.00000318 | 580 |
| Loss of Function | 2.08 | 7 | 15.9 | 0.439 | 9.44e-7 | 187 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000063 | 0.000062 | rare |
| South Asian | 0.000035 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a link between the F-actin cytoskeleton and the extracellular matrix.;
- Disease
- DISEASE: Limb-girdle muscular dystrophy 2F (LGMD2F) [MIM:601287]: An autosomal recessive degenerative myopathy initially affecting the proximal limb girdle musculature. Muscle from patients shows a complete loss of delta-sarcoglycan as well as of the others components of the sarcoglycan complex. {ECO:0000269|PubMed:9832045}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1L (CMD1L) [MIM:606685]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:10974018}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.368
Intolerance Scores
- LoFtool
- 0.276
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 34.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.789
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |